- Filename
- 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased.bcftools_stats.txt
- Full Path
- s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp_atx_exp0001/tools_daq_bams__8a99ba01--20260203-171151/reports/raw_qc/bcftools/mutect2/1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08/1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased.bcftools_stats.txt
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- 10.5 KB
- Published
- Feb 03, 2026 10:35 PM
# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased.vcf.gz
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 1029_2LI-T1-TDNA-1_23FC2GLT4_s08_vs_1029_2LI-N1-BDNA-1_2375WFLT3_s08.mutect2.whatshap.phased.vcf.gz
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 2
SN 0 number of records: 8796
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 5083
SN 0 number of MNPs: 537
SN 0 number of indels: 3469
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1402
SN 0 number of multiallelic SNP sites: 57
# TSTV, transitions/transversions:
# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 3510 1636 2.15 3395 1473 2.30
# SiS, Singleton stats:
# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
SiS 0 1 5146 3510 1636 7094 0 0 7094
# AF, Stats by non-reference allele frequency:
# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
AF 0 0.000000 5146 3510 1636 7094 0 0 7094
# QUAL, Stats by quality
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 . 4868 3395 1473 3469
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -60 44 0 .
IDD 0 -59 1 0 .
IDD 0 -58 2 0 .
IDD 0 -57 1 0 .
IDD 0 -56 1 0 .
IDD 0 -54 2 0 .
IDD 0 -53 1 0 .
IDD 0 -50 1 0 .
IDD 0 -49 1 0 .
IDD 0 -48 3 0 .
IDD 0 -47 1 0 .
IDD 0 -45 1 0 .
IDD 0 -42 4 0 .
IDD 0 -41 1 0 .
IDD 0 -39 4 0 .
IDD 0 -38 1 0 .
IDD 0 -36 5 0 .
IDD 0 -33 1 0 .
IDD 0 -30 6 0 .
IDD 0 -29 1 0 .
IDD 0 -27 4 0 .
IDD 0 -26 2 0 .
IDD 0 -24 6 0 .
IDD 0 -21 6 0 .
IDD 0 -20 3 0 .
IDD 0 -18 8 0 .
IDD 0 -17 1 0 .
IDD 0 -16 4 0 .
IDD 0 -15 11 0 .
IDD 0 -14 9 0 .
IDD 0 -13 5 0 .
IDD 0 -12 29 0 .
IDD 0 -11 10 0 .
IDD 0 -10 30 0 .
IDD 0 -9 41 0 .
IDD 0 -8 71 0 .
IDD 0 -7 33 0 .
IDD 0 -6 307 0 .
IDD 0 -5 163 0 .
IDD 0 -4 393 0 .
IDD 0 -3 1687 0 .
IDD 0 -2 897 0 .
IDD 0 -1 1070 0 .
IDD 0 1 959 0 .
IDD 0 2 704 0 .
IDD 0 3 222 0 .
IDD 0 4 117 0 .
IDD 0 5 21 0 .
IDD 0 6 48 0 .
IDD 0 7 9 0 .
IDD 0 8 25 0 .
IDD 0 9 12 0 .
IDD 0 10 14 0 .
IDD 0 11 1 0 .
IDD 0 12 10 0 .
IDD 0 13 3 0 .
IDD 0 14 10 0 .
IDD 0 15 4 0 .
IDD 0 16 7 0 .
IDD 0 17 2 0 .
IDD 0 18 8 0 .
IDD 0 19 1 0 .
IDD 0 20 2 0 .
IDD 0 21 1 0 .
IDD 0 24 2 0 .
IDD 0 25 1 0 .
IDD 0 27 1 0 .
IDD 0 28 2 0 .
IDD 0 29 3 0 .
IDD 0 30 5 0 .
IDD 0 31 1 0 .
IDD 0 32 1 0 .
IDD 0 35 1 0 .
IDD 0 42 1 0 .
IDD 0 43 1 0 .
IDD 0 44 1 0 .
IDD 0 45 1 0 .
IDD 0 48 1 0 .
IDD 0 52 1 0 .
IDD 0 54 1 0 .
IDD 0 57 1 0 .
IDD 0 60 17 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 170
ST 0 A>G 526
ST 0 A>T 171
ST 0 C>A 256
ST 0 C>G 189
ST 0 C>T 1232
ST 0 G>A 1254
ST 0 G>C 229
ST 0 G>T 256
ST 0 T>A 197
ST 0 T>C 498
ST 0 T>G 168
# DP, Depth distribution
# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
DP 0 19 0 0.000000 1 0.011369
DP 0 21 0 0.000000 3 0.034106
DP 0 22 0 0.000000 1 0.011369
DP 0 24 0 0.000000 1 0.011369
DP 0 25 0 0.000000 1 0.011369
DP 0 29 0 0.000000 1 0.011369
DP 0 32 0 0.000000 1 0.011369
DP 0 33 0 0.000000 2 0.022738
DP 0 34 0 0.000000 3 0.034106
DP 0 35 0 0.000000 1 0.011369
DP 0 37 0 0.000000 1 0.011369
DP 0 38 0 0.000000 1 0.011369
DP 0 42 0 0.000000 1 0.011369
DP 0 46 0 0.000000 1 0.011369
DP 0 51 0 0.000000 1 0.011369
DP 0 52 0 0.000000 1 0.011369
DP 0 56 0 0.000000 1 0.011369
DP 0 58 0 0.000000 3 0.034106
DP 0 60 0 0.000000 1 0.011369
DP 0 61 0 0.000000 1 0.011369
DP 0 62 0 0.000000 1 0.011369
DP 0 64 0 0.000000 1 0.011369
DP 0 65 0 0.000000 2 0.022738
DP 0 66 0 0.000000 2 0.022738
DP 0 68 0 0.000000 1 0.011369
DP 0 69 0 0.000000 2 0.022738
DP 0 70 0 0.000000 1 0.011369
DP 0 71 0 0.000000 1 0.011369
DP 0 73 0 0.000000 1 0.011369
DP 0 78 0 0.000000 1 0.011369
DP 0 83 0 0.000000 1 0.011369
DP 0 86 0 0.000000 1 0.011369
DP 0 87 0 0.000000 1 0.011369
DP 0 90 0 0.000000 1 0.011369
DP 0 92 0 0.000000 1 0.011369
DP 0 97 0 0.000000 1 0.011369
DP 0 104 0 0.000000 1 0.011369
DP 0 109 0 0.000000 1 0.011369
DP 0 125 0 0.000000 2 0.022738
DP 0 138 0 0.000000 1 0.011369
DP 0 143 0 0.000000 1 0.011369
DP 0 146 0 0.000000 1 0.011369
DP 0 152 0 0.000000 2 0.022738
DP 0 154 0 0.000000 1 0.011369
DP 0 158 0 0.000000 1 0.011369
DP 0 164 0 0.000000 1 0.011369
DP 0 166 0 0.000000 1 0.011369
DP 0 168 0 0.000000 1 0.011369
DP 0 170 0 0.000000 1 0.011369
DP 0 181 0 0.000000 1 0.011369
DP 0 183 0 0.000000 1 0.011369
DP 0 184 0 0.000000 1 0.011369
DP 0 186 0 0.000000 1 0.011369
DP 0 187 0 0.000000 2 0.022738
DP 0 188 0 0.000000 1 0.011369
DP 0 189 0 0.000000 1 0.011369
DP 0 193 0 0.000000 1 0.011369
DP 0 194 0 0.000000 1 0.011369
DP 0 203 0 0.000000 1 0.011369
DP 0 209 0 0.000000 1 0.011369
DP 0 210 0 0.000000 1 0.011369
DP 0 215 0 0.000000 1 0.011369
DP 0 220 0 0.000000 1 0.011369
DP 0 221 0 0.000000 1 0.011369
DP 0 224 0 0.000000 1 0.011369
DP 0 232 0 0.000000 1 0.011369
DP 0 234 0 0.000000 1 0.011369
DP 0 235 0 0.000000 1 0.011369
DP 0 238 0 0.000000 1 0.011369
DP 0 240 0 0.000000 1 0.011369
DP 0 242 0 0.000000 2 0.022738
DP 0 246 0 0.000000 1 0.011369
DP 0 248 0 0.000000 1 0.011369
DP 0 249 0 0.000000 2 0.022738
DP 0 250 0 0.000000 1 0.011369
DP 0 251 0 0.000000 1 0.011369
DP 0 253 0 0.000000 1 0.011369
DP 0 255 0 0.000000 1 0.011369
DP 0 256 0 0.000000 1 0.011369
DP 0 261 0 0.000000 1 0.011369
DP 0 264 0 0.000000 1 0.011369
DP 0 268 0 0.000000 1 0.011369
DP 0 275 0 0.000000 1 0.011369
DP 0 283 0 0.000000 2 0.022738
DP 0 287 0 0.000000 2 0.022738
DP 0 288 0 0.000000 1 0.011369
DP 0 289 0 0.000000 1 0.011369
DP 0 290 0 0.000000 1 0.011369
DP 0 293 0 0.000000 1 0.011369
DP 0 294 0 0.000000 1 0.011369
DP 0 295 0 0.000000 1 0.011369
DP 0 298 0 0.000000 1 0.011369
DP 0 306 0 0.000000 1 0.011369
DP 0 310 0 0.000000 1 0.011369
DP 0 312 0 0.000000 1 0.011369
DP 0 313 0 0.000000 1 0.011369
DP 0 315 0 0.000000 1 0.011369
DP 0 316 0 0.000000 1 0.011369
DP 0 320 0 0.000000 1 0.011369
DP 0 325 0 0.000000 2 0.022738
DP 0 328 0 0.000000 1 0.011369
DP 0 334 0 0.000000 2 0.022738
DP 0 336 0 0.000000 1 0.011369
DP 0 340 0 0.000000 2 0.022738
DP 0 342 0 0.000000 2 0.022738
DP 0 343 0 0.000000 1 0.011369
DP 0 349 0 0.000000 1 0.011369
DP 0 351 0 0.000000 3 0.034106
DP 0 352 0 0.000000 1 0.011369
DP 0 359 0 0.000000 2 0.022738
DP 0 360 0 0.000000 2 0.022738
DP 0 361 0 0.000000 1 0.011369
DP 0 362 0 0.000000 2 0.022738
DP 0 364 0 0.000000 1 0.011369
DP 0 366 0 0.000000 2 0.022738
DP 0 367 0 0.000000 1 0.011369
DP 0 368 0 0.000000 1 0.011369
DP 0 369 0 0.000000 1 0.011369
DP 0 376 0 0.000000 2 0.022738
DP 0 378 0 0.000000 1 0.011369
DP 0 379 0 0.000000 4 0.045475
DP 0 381 0 0.000000 2 0.022738
DP 0 382 0 0.000000 2 0.022738
DP 0 383 0 0.000000 1 0.011369
DP 0 384 0 0.000000 1 0.011369
DP 0 385 0 0.000000 4 0.045475
DP 0 386 0 0.000000 2 0.022738
DP 0 387 0 0.000000 1 0.011369
DP 0 388 0 0.000000 1 0.011369
DP 0 393 0 0.000000 1 0.011369
DP 0 394 0 0.000000 1 0.011369
DP 0 395 0 0.000000 1 0.011369
DP 0 396 0 0.000000 1 0.011369
DP 0 397 0 0.000000 3 0.034106
DP 0 398 0 0.000000 2 0.022738
DP 0 399 0 0.000000 1 0.011369
DP 0 402 0 0.000000 2 0.022738
DP 0 405 0 0.000000 3 0.034106
DP 0 406 0 0.000000 1 0.011369
DP 0 407 0 0.000000 1 0.011369
DP 0 408 0 0.000000 1 0.011369
DP 0 411 0 0.000000 1 0.011369
DP 0 412 0 0.000000 2 0.022738
DP 0 413 0 0.000000 3 0.034106
DP 0 414 0 0.000000 2 0.022738
DP 0 417 0 0.000000 1 0.011369
DP 0 418 0 0.000000 1 0.011369
DP 0 419 0 0.000000 1 0.011369
DP 0 420 0 0.000000 1 0.011369
DP 0 421 0 0.000000 2 0.022738
DP 0 422 0 0.000000 1 0.011369
DP 0 425 0 0.000000 2 0.022738
DP 0 427 0 0.000000 2 0.022738
DP 0 428 0 0.000000 1 0.011369
DP 0 430 0 0.000000 1 0.011369
DP 0 432 0 0.000000 1 0.011369
DP 0 433 0 0.000000 3 0.034106
DP 0 434 0 0.000000 3 0.034106
DP 0 435 0 0.000000 2 0.022738
DP 0 436 0 0.000000 2 0.022738
DP 0 438 0 0.000000 1 0.011369
DP 0 439 0 0.000000 1 0.011369
DP 0 440 0 0.000000 4 0.045475
DP 0 441 0 0.000000 3 0.034106
DP 0 442 0 0.000000 1 0.011369
DP 0 443 0 0.000000 3 0.034106
DP 0 446 0 0.000000 1 0.011369
DP 0 447 0 0.000000 2 0.022738
DP 0 448 0 0.000000 1 0.011369
DP 0 449 0 0.000000 1 0.011369
DP 0 450 0 0.000000 3 0.034106
DP 0 451 0 0.000000 1 0.011369
DP 0 452 0 0.000000 1 0.011369
DP 0 453 0 0.000000 2 0.022738
DP 0 455 0 0.000000 2 0.022738
DP 0 456 0 0.000000 2 0.022738
DP 0 458 0 0.000000 3 0.034106
DP 0 460 0 0.000000 1 0.011369
DP 0 461 0 0.000000 1 0.011369
DP 0 462 0 0.000000 1 0.011369
DP 0 463 0 0.000000 2 0.022738
DP 0 464 0 0.000000 2 0.022738
DP 0 466 0 0.000000 1 0.011369
DP 0 468 0 0.000000 2 0.022738
DP 0 469 0 0.000000 1 0.011369
DP 0 470 0 0.000000 2 0.022738
DP 0 471 0 0.000000 3 0.034106
DP 0 472 0 0.000000 3 0.034106
DP 0 473 0 0.000000 1 0.011369
DP 0 474 0 0.000000 3 0.034106
DP 0 475 0 0.000000 2 0.022738
DP 0 476 0 0.000000 5 0.056844
DP 0 479 0 0.000000 2 0.022738
DP 0 480 0 0.000000 1 0.011369
DP 0 482 0 0.000000 1 0.011369
DP 0 483 0 0.000000 1 0.011369
DP 0 485 0 0.000000 1 0.011369
DP 0 486 0 0.000000 2 0.022738
DP 0 487 0 0.000000 2 0.022738
DP 0 488 0 0.000000 2 0.022738
DP 0 489 0 0.000000 1 0.011369
DP 0 490 0 0.000000 2 0.022738
DP 0 491 0 0.000000 2 0.022738
DP 0 492 0 0.000000 1 0.011369
DP 0 493 0 0.000000 1 0.011369
DP 0 494 0 0.000000 1 0.011369
DP 0 495 0 0.000000 1 0.011369
DP 0 496 0 0.000000 3 0.034106
DP 0 498 0 0.000000 3 0.034106
DP 0 499 0 0.000000 2 0.022738
DP 0 500 0 0.000000 3 0.034106
DP 0 >500 0 0.000000 8486 96.475671